Computational identification and comparative analysis of miRNA precursors in three palm species
MicroRNAs are small RNAs of 20–25 nucleotides in length, with important functions in the regulation of gene expression. Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnolog...
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| Veröffentlicht in: | Planta 2016-05, Vol.243 (5), p.1265-1277 |
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| creator | da Silva, Aline Cunha Grativol, Clícia Thiebaut, Flávia Hemerly, Adriana Silva Ferreira, Paulo Cavalcanti Gomes |
| description | MicroRNAs are small RNAs of 20–25 nucleotides in length, with important functions in the regulation of gene expression. Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnological tools in palm trees breeding. The goal of this study is the identification of miRNA precursors in the genomes of these species and their possible biological roles suggested by the mature miRNA-based regulation of target genes. Mature miRNA sequences from Arabidopsis thaliana, Oryza sativa, and Zea mays available at the miRBase were used to predict microRNA precursors in the palm genomes. Three hundred and thirty-eight precursors, ranging from 76 to 220 nucleotide (nt) in size and distributed in 33 families were identified. Moreover, we also identified 266 miRNA precursors of Musa acuminata, which are phylogenetically close to palms species. To understand the biological function of palm miRNAs, 374 putative miRNA targets were identified. An enrichment analysis of target-gene function was carried out using the agriGO tool. The results showed that the targets are involved in plant developmental processes, mainly regulating root development. Our findings contribute to increase the knowledge on microRNA roles in palm biology and could help breeding programs of palm trees. |
| doi_str_mv | 10.1007/s00425-016-2486-6 |
| format | Article |
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Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnological tools in palm trees breeding. The goal of this study is the identification of miRNA precursors in the genomes of these species and their possible biological roles suggested by the mature miRNA-based regulation of target genes. Mature miRNA sequences from Arabidopsis thaliana, Oryza sativa, and Zea mays available at the miRBase were used to predict microRNA precursors in the palm genomes. Three hundred and thirty-eight precursors, ranging from 76 to 220 nucleotide (nt) in size and distributed in 33 families were identified. Moreover, we also identified 266 miRNA precursors of Musa acuminata, which are phylogenetically close to palms species. To understand the biological function of palm miRNAs, 374 putative miRNA targets were identified. An enrichment analysis of target-gene function was carried out using the agriGO tool. The results showed that the targets are involved in plant developmental processes, mainly regulating root development. Our findings contribute to increase the knowledge on microRNA roles in palm biology and could help breeding programs of palm trees.</description><identifier>ISSN: 0032-0935</identifier><identifier>EISSN: 1432-2048</identifier><identifier>DOI: 10.1007/s00425-016-2486-6</identifier><identifier>PMID: 26919984</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Science + Business Media</publisher><subject>Agriculture ; Arabidopsis thaliana ; Arecaceae - genetics ; Base Sequence ; Biomedical and Life Sciences ; Biotechnology ; Computational Biology - methods ; Conserved Sequence - genetics ; Ecology ; Elaeis guineensis ; Elaeis oleifera ; Forestry ; Gene Expression Regulation, Plant ; Life Sciences ; MicroRNAs ; Musa - genetics ; Musa acuminata ; ORIGINAL ARTICLE ; Oryza sativa ; Phoeniceae - genetics ; Phoenix dactylifera ; Plant Sciences ; RNA Precursors ; RNA, Plant ; Root development ; Zea mays</subject><ispartof>Planta, 2016-05, Vol.243 (5), p.1265-1277</ispartof><rights>Springer-Verlag Berlin Heidelberg 2016</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c427t-85c211ff9c636381b7dbdd9754bf66ee5caf344d1dd2f1d78cce044d9876e7673</citedby><cites>FETCH-LOGICAL-c427t-85c211ff9c636381b7dbdd9754bf66ee5caf344d1dd2f1d78cce044d9876e7673</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/48726491$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/48726491$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,803,27924,27925,41488,42557,51319,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26919984$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>da Silva, Aline Cunha</creatorcontrib><creatorcontrib>Grativol, Clícia</creatorcontrib><creatorcontrib>Thiebaut, Flávia</creatorcontrib><creatorcontrib>Hemerly, Adriana Silva</creatorcontrib><creatorcontrib>Ferreira, Paulo Cavalcanti Gomes</creatorcontrib><title>Computational identification and comparative analysis of miRNA precursors in three palm species</title><title>Planta</title><addtitle>Planta</addtitle><addtitle>Planta</addtitle><description>MicroRNAs are small RNAs of 20–25 nucleotides in length, with important functions in the regulation of gene expression. Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnological tools in palm trees breeding. The goal of this study is the identification of miRNA precursors in the genomes of these species and their possible biological roles suggested by the mature miRNA-based regulation of target genes. Mature miRNA sequences from Arabidopsis thaliana, Oryza sativa, and Zea mays available at the miRBase were used to predict microRNA precursors in the palm genomes. Three hundred and thirty-eight precursors, ranging from 76 to 220 nucleotide (nt) in size and distributed in 33 families were identified. Moreover, we also identified 266 miRNA precursors of Musa acuminata, which are phylogenetically close to palms species. To understand the biological function of palm miRNAs, 374 putative miRNA targets were identified. An enrichment analysis of target-gene function was carried out using the agriGO tool. The results showed that the targets are involved in plant developmental processes, mainly regulating root development. Our findings contribute to increase the knowledge on microRNA roles in palm biology and could help breeding programs of palm trees.</description><subject>Agriculture</subject><subject>Arabidopsis thaliana</subject><subject>Arecaceae - genetics</subject><subject>Base Sequence</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Computational Biology - methods</subject><subject>Conserved Sequence - genetics</subject><subject>Ecology</subject><subject>Elaeis guineensis</subject><subject>Elaeis oleifera</subject><subject>Forestry</subject><subject>Gene Expression Regulation, Plant</subject><subject>Life Sciences</subject><subject>MicroRNAs</subject><subject>Musa - genetics</subject><subject>Musa acuminata</subject><subject>ORIGINAL ARTICLE</subject><subject>Oryza sativa</subject><subject>Phoeniceae - genetics</subject><subject>Phoenix dactylifera</subject><subject>Plant Sciences</subject><subject>RNA Precursors</subject><subject>RNA, Plant</subject><subject>Root development</subject><subject>Zea mays</subject><issn>0032-0935</issn><issn>1432-2048</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkU1rFTEYhYMo9lr9AS6UgBs3o_mafCzLxS8oLRRdh9zkjeYyMxmTGaH_3rRTi7iQrpKT9znnhRyEXlLyjhKi3ldCBOs7QmXHhJadfIR2VHDWMSL0Y7QjpN2J4f0JelbrkZA2VOopOmHSUGO02CG7z-O8Lm5JeXIDTgGmJcXkbx-wmwL2DXCl6V_QtBuua6o4Rzymq4szPBfwa6m5VJwmvPwoAHh2w4jrDD5BfY6eRDdUeHF3nqJvHz983X_uzi8_fdmfnXdeMLV0uveM0hiNl1xyTQ8qHEIwqheHKCVA713kQgQaAos0KO09kKaNVhKUVPwUvd1y55J_rlAXO6bqYRjcBHmtliojhOGK6gegmnNBjegb-uYf9JjX0j7hlmJESy1po-hG-ZJrLRDtXNLoyrWlxN4UZbeibCvK3hRlZfO8vkteDyOEe8efZhrANqC20fQdyl-r_5P6ajMd65LLfajQiklhKP8NaHenuw</recordid><startdate>20160501</startdate><enddate>20160501</enddate><creator>da Silva, Aline Cunha</creator><creator>Grativol, Clícia</creator><creator>Thiebaut, Flávia</creator><creator>Hemerly, Adriana Silva</creator><creator>Ferreira, Paulo Cavalcanti Gomes</creator><general>Springer Science + Business Media</general><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7TM</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20160501</creationdate><title>Computational identification and comparative analysis of miRNA precursors in three palm species</title><author>da Silva, Aline Cunha ; 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Recent genome sequencing of the palm species Elaeis guineensis, Elaeis oleifera and Phoenix dactylifera have enabled the discovery of miRNA genes, which can be used as biotechnological tools in palm trees breeding. The goal of this study is the identification of miRNA precursors in the genomes of these species and their possible biological roles suggested by the mature miRNA-based regulation of target genes. Mature miRNA sequences from Arabidopsis thaliana, Oryza sativa, and Zea mays available at the miRBase were used to predict microRNA precursors in the palm genomes. Three hundred and thirty-eight precursors, ranging from 76 to 220 nucleotide (nt) in size and distributed in 33 families were identified. Moreover, we also identified 266 miRNA precursors of Musa acuminata, which are phylogenetically close to palms species. To understand the biological function of palm miRNAs, 374 putative miRNA targets were identified. An enrichment analysis of target-gene function was carried out using the agriGO tool. The results showed that the targets are involved in plant developmental processes, mainly regulating root development. Our findings contribute to increase the knowledge on microRNA roles in palm biology and could help breeding programs of palm trees.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Science + Business Media</pub><pmid>26919984</pmid><doi>10.1007/s00425-016-2486-6</doi><tpages>13</tpages></addata></record> |
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| subjects | Agriculture Arabidopsis thaliana Arecaceae - genetics Base Sequence Biomedical and Life Sciences Biotechnology Computational Biology - methods Conserved Sequence - genetics Ecology Elaeis guineensis Elaeis oleifera Forestry Gene Expression Regulation, Plant Life Sciences MicroRNAs Musa - genetics Musa acuminata ORIGINAL ARTICLE Oryza sativa Phoeniceae - genetics Phoenix dactylifera Plant Sciences RNA Precursors RNA, Plant Root development Zea mays |
| title | Computational identification and comparative analysis of miRNA precursors in three palm species |
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